title: Detection of DNA by scraping the formalin-fixed paraffin-embedded tissue.
abstract: BACKGROUND
  Pakistan is a developing country and most of the research laboratories have limited required infrastructures for the diagnosis of cancer at molecular level. The polymerase chain reaction (PCR) on formalin-fixed paraffin-embedded tissues is becoming a popular procedure in the research centres. The study was conducted to introduce two new methods of DNA extraction for the PCR from formalin-fixed paraffin-embedded sections of surgical pathology specimens.
  
  
  METHODS
  Two methods of DNA detection were used. In method A the formalin-fixed tissues were grossed, proper sections were taken, processed in an automatic tissue processor, embedded in paraffin blocks, and microtomic sections were made. In method B, the procedure was the same until embedding in the paraffin blocks, after which the selected paraffin blocks were set on a black card paper (4 cm x 4 cm) and 1 mg of pure scraped tissue was obtained using a scalpel, manually without using microtone.
  
  
  RESULTS
  DNA was successfully extracted but point mutation of p53 gene was not seen in SCP while it was determined in 96 and 93.75 per cent cases of SCC by method A and method B respectively. There was no statistical difference in the results by both methods (P = 0.359).
  
  
  CONCLUSIONS
  Scraping of the tissue for DNA detection was a simple method and may be performed in any laboratory. The reliability, reproducibility, and quality assurance of the present results are consistent with the already established techniques of DNA extraction for PCR.
authors.affiliation: Department of Pathology, King Edward Medical University, Lahore, Pakistan. drmhbukhari@yahoo.com
authors.forename: M H
authors.initials: MH
authors.lastname: Bukhari
authors.forename: S
authors.initials: S
authors.lastname: Niazi
authors.forename: R
authors.initials: R
authors.lastname: Ghani
authors.forename: Z
authors.initials: Z
authors.lastname: Rathore
authors.forename: R
authors.initials: R
authors.lastname: Basharat
authors.forename: N A
authors.initials: NA
authors.lastname: Chaudhry
authors.forename: S
authors.initials: S
authors.lastname: Naeem
mesh_terms: D002294:Carcinoma, Squamous Cell / Q000235:genetics* / Q000378:metabolism*; D045744:Cell Line, Tumor; D004247:DNA / Q000235:genetics* / Q000302:isolation & purification; D005404:Fixatives; D005557:Formaldehyde; D006801:Humans; D016612:Paraffin Embedding / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods*; D016159:Tumor Suppressor Protein p53 / Q000235:genetics* / Q000378:metabolism
chemical_list: D005404:Fixatives; C495901:TP53 protein, human; D016159:Tumor Suppressor Protein p53; D005557:Formaldehyde; D004247:DNA